5GID

Crystal structure of VDR in complex with DLAM-4 (C2 form)

• PDB DOI: https://doi.org/10.2210/pdb5GID/pdb

• Classification: TRANSCRIPTION
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-23 Released: 2016-12-07 
• Deposition Author(s): Asano, L., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.233 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

Regulation of the vitamin D receptor by vitamin D lactam derivatives.

Asano, L., Waku, T., Abe, R., Kuwabara, N., Ito, I., Yanagisawa, J., Nagasawa, K., Shimizu, T.

(2016) FEBS Lett 590: 3270-3279

• PubMed: 27500498 
• DOI: https://doi.org/10.1002/1873-3468.12348
• Primary Citation of Related Structures:  
  5GIC, 5GID, 5GIE


• PubMed Abstract: 
  

  The active metabolite of vitamin D3 , 1α,25-dihydroxyvitamin D3 , acts as a ligand for the vitamin D receptor (VDR) and activates VDR-mediated gene expression. Recently, we characterized 1α,25-dihydroxyvitamin D3 -26,23-lactams (DLAMs), which mimic vitamin D3 metabolites, as noncalcemic VDR ligands that barely activate the receptor. In this study, we present structural insights onto the regulation of VDR function by DLAMs. X-ray crystallographic analysis revealed that DLAMs induced a large conformational change in the loop region between helices H6 and H7 in the VDR ligand-binding domain. Our structural analysis suggests that targeting of the loop region may be a new mode of VDR regulation.

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Organizational Affiliation: 

Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.92 kDa 
• Atom Count: 1,987 
• Modelled Residue Count: 246 
• Deposited Residue Count: 258 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	249	Rattus norvegicus	Mutation(s): 0  Gene Names: Vdr, Nr1i1
UniProt
Find proteins for P13053 (Rattus norvegicus) Explore P13053  Go to UniProtKB:  P13053

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SRC1	B [auth C]	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens) Explore Q15648  Go to UniProtKB:  Q15648
PHAROS:  Q15648 GTEx:  ENSG00000125686

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VDP	C [auth A]	(3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one C37 H53 N O4 IVUJLUOFPHOBPG-HEMHZJQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.233 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.51	α = 90
b = 42.345	β = 96.46
c = 42.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Asano, L., Shimizu, T.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references